kottke.org posts about DNA

Genome editing started with just a few big labs putting in lots of effort, trying something 1,000 times for one or two successes. Now it's something that someone with a BS and a couple thousand dollars' worth of equipment can do. What was impractical is now almost everyday. That's a big deal.

"What it begins to suggest is that we're looking at a Lord of the Rings-type world -- that there were many hominid populations," says Mark Thomas, an evolutionary geneticist at University College London who was at the meeting but was not involved in the work.

But, more interestingly, the analysis also detected the Denisovans also bred with an as-yet-unknown species of humans.

The Denisovan genome indicates that the population got around: Reich said at the meeting that as well as interbreeding with the ancestors of Oceanians, they also bred with Neanderthals and the ancestors of modern humans in China and other parts of East Asia. Most surprisingly, Reich said, the genomes indicate that Denisovans interbred with yet another extinct population of archaic humans that lived in Asia more than 30,000 years ago -- one that is neither human nor Neanderthal.

Is this the first time a new human species has been discovered through DNA evidence alone?

Hailed as a breakthrough by other scientists, the work is a step towards the synthesis of cells able to churn out drugs and other useful molecules. It also raises the possibility that cells could one day be engineered without any of the four DNA bases used by all organisms on Earth.

"What we have now is a living cell that literally stores increased genetic information," says Floyd Romesberg, a chemical biologist at the Scripps Research Institute in La Jolla, California, who led the 15-year effort.

So instead of just using the GATTACA alphabet, scientists may eventually gain the use of an alphabet containing dozens or even hundreds or thousands of different letters. Potentially powerful stuff.

Did you know that there are new human beings? Like, not just new human babies but new species of humans? And not just new species of humans, but new species of humans who lived at the same time as, and even possibly bred with, modern humans, aka us? (Helloooooo, mesofacts.)

If you've read kottke.org over the years, you've likely heard of Homo floresiensis (aka Flores man, aka Hobbits), a species whose remains were discovered in present-day Indonesia in 2003. Homo floresiensis lived 95,000 to 13,000 years ago and stood about three feet high.

In this month's National Geographic, Jamie Shreeve tells the story of the 2010 discovery of the Denisovans, hominids who lived in modern-day Russia as late as 40,000 years ago. Only a handful of bone fragments and teeth have been recovered, but DNA and other evidence suggests that Denisovans, Neanderthals, and modern humans lived together in the same place and interbred.

By the time of the Denisova symposium, Pääbo and his colleagues had published first drafts of the entire Neanderthal and Denisovan genomes. Reading so many more pages allowed Pääbo and his colleagues, including David Reich at Harvard University and Montgomery Slatkin at the University of California, Berkeley, to discover that human genomes today actually contain a small but significant amount of Neanderthal code -- on average about 2.5 percent. The Neanderthals still may have been swept into extinction by the strange, high-browed new people who followed them out of Africa, but not before some commingling that left a little Neanderthal in most of us, 50,000 years later. Only one group of modern humans escaped that influence: Africans, because the commingling happened outside that continent.

Although the Denisovans' genome showed that they were more closely related to the Neanderthals, they too had left their mark on us. But the geographic pattern of that legacy was odd. When the researchers compared the Denisovan genome with those of various modern human populations, they found no trace of it in Russia or nearby China, or anywhere else, for that matter -- except in the genomes of New Guineans, other people from islands in Melanesia, and Australian Aborigines. On average their genomes are about 5 percent Denisovan. Negritos in the Philippines have as much as 2.5 percent.

The Red Deer Cave dwellers' unusual features included a flat face, a broad nose, a jutting jaw that lacked a chin, large molar teeth, a rounded braincase with prominent brow ridges, and thick skull bones, the researchers say.

Their brains were "moderate in size," Curnoe added.

Despite this seemingly primitive human design, radiocarbon dating of charcoal from the fossil deposits suggests the Red Deer Cave people lived just 14,500 to 11,500 years ago, the team says-a time by which all other human species, such as Neanderthals, are thought to have died out.

As with the other potential new human species, and as is proper in science, there is some skepticism about the Red Deer Cave people.

The team's suggestion that the Red Deer Cave people are somehow evolutionarily unique is receiving a skeptical reception from other scientists.

Physical anthropologist Erik Trinkaus described the findings as "an unfortunate overinterpretation and misinterpretation of robust early modern humans, probably with affinities to modern Melanesians"-indigenous peoples of Pacific islands stretching from New Guinea to Fiji (map).

"There is nothing extraordinary" about the newly announced fossil human, added Trinkaus, of Washington University in St. Louis, via email.

Heather Dewey-Hagborg collects hair, chewed gum, and smoked cigarettes, pulls the DNA out of them, and uses the genetic information to produce models of what the people who used those items might have looked like.

From this sequence, Dewey-Hagborg gathers information about the person's ancestry, gender, eye color, propensity to be overweight and other traits related to facial morphology, such as the space between one's eyes. "I have a list of about 40 or 50 different traits that I have either successfully analyzed or I am in the process of working on right now," she says.

Dewey-Hagborg then enters these parameters into a computer program to create a 3D model of the person's face." Ancestry gives you most of the generic picture of what someone is going to tend to look like. Then, the other traits point towards modifications on that kind of generic portrait," she explains. The artist ultimately sends a file of the 3D model to a 3D printer on the campus of her alma mater, New York University, so that it can be transformed into sculpture.

By comparing the specimens' ages and degrees of DNA degradation, the researchers calculated that DNA has a half-life of 521 years. That means that after 521 years, half of the bonds between nucleotides in the backbone of a sample would have broken; after another 521 years half of the remaining bonds would have gone; and so on.

The team predicts that even in a bone at an ideal preservation temperature of -5 ºC, effectively every bond would be destroyed after a maximum of 6.8 million years. The DNA would cease to be readable much earlier -- perhaps after roughly 1.5 million years, when the remaining strands would be too short to give meaningful information.

In the last few years, scientists have discovered that before Neanderthals went extinct around 30,000 years ago, they interbred with modern humans. As a result, many humans alive today contain Neanderthal DNA in their genomes, typically between 1-4%.

Yesterday, a few of the editors at The Atlantic had their genes analyzed for Neanderthal DNA: Alexis Madrigal had 3.6%, Steve Clemons had 4.3%, and James Fallows had 5%. Personal genetic information company 23andMe added the ability to determine your Neanderthal DNA percentage a few months ago and it turns out 2.7% of my DNA is from Neanderthals, compared to 2.5% for the average 23andMe user.

If you have a 23andMe acct, you can check your percentage by logging in and going to "Ancestry Labs" in the sidebar.

So many choices. Which car insurance. Which cereal. Which deodorant, toothpaste, toothbrush, soap, shampoo. Rows and rows of products. Varieties, sizes, colors. Which is cheaper? Which is better? What's the best buy? Which gum to chew? When he went into prison there were, like, two kinds of chewing gum. Now there are a zillion. One of the small gifts he gives himself is trying all the gums. "I can spoil myself a little so long as I stay within my means," he says. Papaya juice! Kiwi and strawberry nectar! Green tea! Arnold Palmer -- he was a golfer when Towler went down. Now he is a drink, sweet and so incredibly thirst quenching.

He loves work. He got out May 5 and started working June 21. Hell, I've been vacationing for thirty years. He wears a smock and pushes a mail cart. He stops at all the cubicles, greets everyone with his friendly smile. Ray even loves commuting to work, especially now, in his new car, a black Ford Focus. He's like a sixteen-year-old who can finally drive himself to school. It costs almost the same to park as it does to take the train.

In 1983, Kary Mullis first developed PCR, for which he later received a Nobel Prize. But the tool is still expensive, even though the technology is almost 30 years old. If computing grew at the same pace, we would all still be paying $2,000+ for a 1 MHz Apple II computer. Innovation in biotech needs a kick start!

When I think about the differences [between me and my adoptive parents], I wonder if they're personality traits I cultivated on my own or if they belong to someone else who passed them onto me. Things like a preference for morning or evening hours can often be genetic, and this is part of what I hope the DNA test will tell me.

I know someone who adopted a baby and they have never told her that she's adopted and don't plan to (she's now in her 20s). When DNA testing becomes commonplace in another 5-15 years, I wonder how long that secret will last and what her reaction will be.

If the genome of an extinct species can be reconstructed, biologists can work out the exact DNA differences with the genome of its nearest living relative. There are talks on how to modify the DNA in an elephant's egg so that after each round of changes it would progressively resemble the DNA in a mammoth egg. The final-stage egg could then be brought to term in an elephant mother, and mammoths might once again roam the Siberian steppes.

The article also notes that if this works for the mammoth, it might also be possible to do the same for a Neanderthal. What an age we live in.

Watched America's Stone Age Explorers on PBS this evening, a summary of recent findings about who the first Americans were, where they came from, and when they arrived. Recent genetic and archeological evidence suggests they arrived earlier than generally accepted and may have originated from Europe rather than Asia.